Hi,
Look under Administration > Site Settings > API Keys
From there you can choose the primary search engine. Click the help file links for more info and notice that you need a Google Custom Search Id to use Google search.
Yes, you are right about syncing files if you are using some kind of farm or cluster where they don't all use the same drive. These are issues to solve before we can make a web farm package for mojoPortal.
Best,
Joe